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Expected output log for the test example
Sina Majidian edited this page Sep 23, 2025
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This is the expected stdout log for the test example.
$ read2tree --tree --standalone_path marker_genes/ --reads sample_1.fastq sample_2.fastq --output_path output --dna_reference dna_ref.fa --debug --tree --threads 1
2025-09-23 15:01:25 INFO ------- Read2Tree version: 2.0.0 -------
2025-09-23 15:01:25 DEBUG Debug mode is on
2025-09-23 15:01:25 INFO sample_1: read2tree was run with: output_path='output', standalone_path='marker_genes/', reads=['sample_1.fastq', 'sample_2.fastq'], read_type='-ax sr', threads=1, sample_reads=False, genome_len=2000000, coverage=10, min_cons_coverage=1, dna_reference='dna_ref.fa', sc_threshold=0.25, debug=True, sequence_selection_mode='sc', species_name='sample_1', tree=True, step='all', min_species=None, remove_species_mapping=None, remove_species_ogs=None, keep_all_ogs=True, ignore_species=None
2025-09-23 15:01:25 INFO Running read2tree in mode all
2025-09-23 15:01:25 INFO sample_1: ------- NEW RUN -------
--- Load OGs with min 0 species from oma marker_genes - mode = marker_genes ---
Loading files for pre-filter: 100%|█████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 1301.67 OGs/s]
2025-09-23 15:01:26 INFO --- Load ogs and find their corresponding DNA seq from dna_ref.fa ---
2025-09-23 15:01:26 INFO Loading dna_ref.fa into memory. This might take a while . . .
Loading OGs: 0%| | 0/20 [00:00<?, ? OGs/s]2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.03947782516479492.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.05063796043395996.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.05960536003112793.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.06969547271728516.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.08430194854736328.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.09534454345703125.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.1026906967163086.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.1093606948852539.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.11684799194335938.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.12622618675231934.
Loading OGs: 50%|████████████████████████████████████████████████ | 10/20 [00:00<00:00, 95.61 OGs/s]2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.13471245765686035.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.14281463623046875.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.15083670616149902.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.16733932495117188.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.1749579906463623.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.1815943717956543.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.1892693042755127.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.19844675064086914.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.205582857131958.
2025-09-23 15:01:26 INFO sample_1: Gathering of DNA seq for 20 OGs took 0.21402359008789062.
Loading OGs: 100%|███████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 103.92 OGs/s]
--- Generating reference for mapping ---
Loading records: 100%|██████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 65638.56 record/s]
2025-09-23 15:01:26 INFO sample_1: Extracted 5 reference species form 20 ogs took 0.0008904933929443359
2025-09-23 15:01:26 INFO --- Alignment of 20 OGs ---
2025-09-23 15:01:26 INFO aligning OG OG1001241 with 5 proteins
2025-09-23 15:01:26 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpfohgl7fh
2025-09-23 15:01:27 INFO aligning OG OG1008242 with 5 proteins
2025-09-23 15:01:27 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmp_op9i46r
2025-09-23 15:01:27 INFO aligning OG OG1065415 with 5 proteins
2025-09-23 15:01:27 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpfv0nxn3y
2025-09-23 15:01:28 INFO aligning OG OG1121053 with 5 proteins
2025-09-23 15:01:28 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmppb3kd85j
2025-09-23 15:01:28 INFO aligning OG OG1125645 with 5 proteins
2025-09-23 15:01:28 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpebn66qq5
2025-09-23 15:01:29 INFO aligning OG OG1133018 with 5 proteins
2025-09-23 15:01:29 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmphi7mj8t6
2025-09-23 15:01:29 INFO aligning OG OG1151179 with 5 proteins
2025-09-23 15:01:29 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpvfng1jem
2025-09-23 15:01:30 INFO aligning OG OG1163384 with 5 proteins
2025-09-23 15:01:30 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpn1ek2u6i
2025-09-23 15:01:30 INFO aligning OG OG1171372 with 5 proteins
2025-09-23 15:01:30 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpppwu4y1a
2025-09-23 15:01:31 INFO aligning OG OG1188079 with 5 proteins
2025-09-23 15:01:31 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmp2zm334dd
2025-09-23 15:01:31 INFO aligning OG OG649157 with 5 proteins
2025-09-23 15:01:31 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmphfpl2yqc
2025-09-23 15:01:32 INFO aligning OG OG649216 with 5 proteins
2025-09-23 15:01:32 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpktccj5fr
2025-09-23 15:01:32 INFO aligning OG OG671579 with 5 proteins
2025-09-23 15:01:32 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpd3bdshi3
2025-09-23 15:01:34 INFO aligning OG OG681083 with 5 proteins
2025-09-23 15:01:34 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpxnk3ol3a
2025-09-23 15:01:34 INFO aligning OG OG681195 with 5 proteins
2025-09-23 15:01:34 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmp3gh31k18
2025-09-23 15:01:35 INFO aligning OG OG683078 with 5 proteins
2025-09-23 15:01:35 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmp9bqk88v4
2025-09-23 15:01:35 INFO aligning OG OG894224 with 5 proteins
2025-09-23 15:01:35 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpjbccgd2q
2025-09-23 15:01:36 INFO aligning OG OG898327 with 5 proteins
2025-09-23 15:01:36 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmp8lj9f137
2025-09-23 15:01:36 INFO aligning OG OG944789 with 5 proteins
2025-09-23 15:01:36 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmpbrg5yxvy
2025-09-23 15:01:37 INFO aligning OG OG974829 with 5 proteins
2025-09-23 15:01:37 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmp3l_sujs9
2025-09-23 15:01:37 INFO sample_1: Alignment of 20 OGs took 11.363831996917725.
2025-09-23 15:01:37 DEBUG Debug mode is on
--- Mapping of reads to reference sequences ---
Mapping reads to species: 0%| | 0/5 [00:00<?, ? species/s]2025-09-23 15:01:37 INFO sample_1: --- Mapping of reads to MNELE reference species ---
2025-09-23 15:01:37 DEBUG Running minimap2 -ax sr -t 1 output/02_ref_dna/MNELE_OGs.fa sample_1.fastq sample_2.fastq > output/04_mapping_sample_1/MNELE_OGs.sam
2025-09-23 15:01:37 DEBUG Shell err: b'[M::mm_idx_gen::0.006*1.61] collected minimizers\n[M::mm_idx_gen::0.009*1.36] sorted minimizers\n[M::main::0.009*1.36] loaded/built the index for 20 target sequence(s)\n[M::mm_mapopt_update::0.009*1.35] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 20\n[M::mm_idx_stat::0.010*1.33] distinct minimizers: 5484 (99.98% are singletons); average occurrences: 1.000; average spacing: 6.131; total length: 33627\n[M::worker_pipeline::0.180*1.01] mapped 50000 sequences\n[M::main] Version: 2.30-r1287\n[M::main] CMD: minimap2 -ax sr -t 1 output/02_ref_dna/MNELE_OGs.fa sample_1.fastq sample_2.fastq\n[M::main] Real time: 0.185 sec; CPU: 0.186 sec; Peak RSS: 0.020 GB\n'
2025-09-23 15:01:37 DEBUG mapping with minimap2 -ax sr -t 1 output/02_ref_dna/MNELE_OGs.fa sample_1.fastq sample_2.fastq > output/04_mapping_sample_1/MNELE_OGs.sam
2025-09-23 15:01:37 INFO sample_1: Mapping to MNELE_OGs.fa references took 0.25930237770080566.
2025-09-23 15:01:37 DEBUG samtools view -F 4 -bh -S -@ 1 -o output/04_mapping_sample_1/MNELE_OGs.bam output/04_mapping_sample_1/MNELE_OGs.sam
2025-09-23 15:01:37 DEBUG Running samtools view -F 4 -bh -S -@ 1 -o output/04_mapping_sample_1/MNELE_OGs.bam output/04_mapping_sample_1/MNELE_OGs.sam
2025-09-23 15:01:38 DEBUG Running samtools sort -@ 1 -o output/04_mapping_sample_1/MNELE_OGs_sorted.bam output/04_mapping_sample_1/MNELE_OGs.bam
2025-09-23 15:01:38 DEBUG Running samtools sort -@ 1 -o output/04_mapping_sample_1/MNELE_OGs_sorted.bam output/04_mapping_sample_1/MNELE_OGs.bam
2025-09-23 15:01:38 DEBUG samtools index -@ 1 output/04_mapping_sample_1/MNELE_OGs_sorted.bam
2025-09-23 15:01:38 DEBUG Running samtools index -@ 1 output/04_mapping_sample_1/MNELE_OGs_sorted.bam
2025-09-23 15:01:38 WARNING No mapped reads on MNELE .
Mapping reads to species: 20%|████████████████▏ | 1/5 [00:00<00:02, 1.76 species/s]2025-09-23 15:01:38 INFO sample_1: --- Mapping of reads to HUMAN reference species ---
2025-09-23 15:01:38 DEBUG Running minimap2 -ax sr -t 1 output/02_ref_dna/HUMAN_OGs.fa sample_1.fastq sample_2.fastq > output/04_mapping_sample_1/HUMAN_OGs.sam
2025-09-23 15:01:38 DEBUG Shell err: b'[M::mm_idx_gen::0.006*1.48] collected minimizers\n[M::mm_idx_gen::0.010*1.29] sorted minimizers\n[M::main::0.010*1.29] loaded/built the index for 20 target sequence(s)\n[M::mm_mapopt_update::0.010*1.29] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 20\n[M::mm_idx_stat::0.011*1.27] distinct minimizers: 6083 (100.00% are singletons); average occurrences: 1.000; average spacing: 6.084; total length: 37008\n[M::worker_pipeline::0.181*1.01] mapped 50000 sequences\n[M::main] Version: 2.30-r1287\n[M::main] CMD: minimap2 -ax sr -t 1 output/02_ref_dna/HUMAN_OGs.fa sample_1.fastq sample_2.fastq\n[M::main] Real time: 0.185 sec; CPU: 0.187 sec; Peak RSS: 0.022 GB\n'
2025-09-23 15:01:38 DEBUG mapping with minimap2 -ax sr -t 1 output/02_ref_dna/HUMAN_OGs.fa sample_1.fastq sample_2.fastq > output/04_mapping_sample_1/HUMAN_OGs.sam
2025-09-23 15:01:38 INFO sample_1: Mapping to HUMAN_OGs.fa references took 0.21886801719665527.
2025-09-23 15:01:38 DEBUG samtools view -F 4 -bh -S -@ 1 -o output/04_mapping_sample_1/HUMAN_OGs.bam output/04_mapping_sample_1/HUMAN_OGs.sam
2025-09-23 15:01:38 DEBUG Running samtools view -F 4 -bh -S -@ 1 -o output/04_mapping_sample_1/HUMAN_OGs.bam output/04_mapping_sample_1/HUMAN_OGs.sam
2025-09-23 15:01:38 DEBUG Running samtools sort -@ 1 -o output/04_mapping_sample_1/HUMAN_OGs_sorted.bam output/04_mapping_sample_1/HUMAN_OGs.bam
2025-09-23 15:01:38 DEBUG Running samtools sort -@ 1 -o output/04_mapping_sample_1/HUMAN_OGs_sorted.bam output/04_mapping_sample_1/HUMAN_OGs.bam
2025-09-23 15:01:38 DEBUG samtools index -@ 1 output/04_mapping_sample_1/HUMAN_OGs_sorted.bam
2025-09-23 15:01:38 DEBUG Running samtools index -@ 1 output/04_mapping_sample_1/HUMAN_OGs_sorted.bam
Mapping reads to species: 40%|████████████████████████████████▍ | 2/5 [00:01<00:01, 2.04 species/s]2025-09-23 15:01:38 INFO sample_1: --- Mapping of reads to RATNO reference species ---
2025-09-23 15:01:38 DEBUG Running minimap2 -ax sr -t 1 output/02_ref_dna/RATNO_OGs.fa sample_1.fastq sample_2.fastq > output/04_mapping_sample_1/RATNO_OGs.sam
2025-09-23 15:01:38 DEBUG Shell err: b'[M::mm_idx_gen::0.005*1.51] collected minimizers\n[M::mm_idx_gen::0.009*1.29] sorted minimizers\n[M::main::0.010*1.29] loaded/built the index for 20 target sequence(s)\n[M::mm_mapopt_update::0.010*1.29] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 20\n[M::mm_idx_stat::0.010*1.27] distinct minimizers: 6160 (100.00% are singletons); average occurrences: 1.000; average spacing: 6.037; total length: 37185\n[M::worker_pipeline::0.179*1.01] mapped 50000 sequences\n[M::main] Version: 2.30-r1287\n[M::main] CMD: minimap2 -ax sr -t 1 output/02_ref_dna/RATNO_OGs.fa sample_1.fastq sample_2.fastq\n[M::main] Real time: 0.184 sec; CPU: 0.186 sec; Peak RSS: 0.021 GB\n'
2025-09-23 15:01:38 DEBUG mapping with minimap2 -ax sr -t 1 output/02_ref_dna/RATNO_OGs.fa sample_1.fastq sample_2.fastq > output/04_mapping_sample_1/RATNO_OGs.sam
2025-09-23 15:01:38 INFO sample_1: Mapping to RATNO_OGs.fa references took 0.2140662670135498.
2025-09-23 15:01:38 DEBUG samtools view -F 4 -bh -S -@ 1 -o output/04_mapping_sample_1/RATNO_OGs.bam output/04_mapping_sample_1/RATNO_OGs.sam
2025-09-23 15:01:38 DEBUG Running samtools view -F 4 -bh -S -@ 1 -o output/04_mapping_sample_1/RATNO_OGs.bam output/04_mapping_sample_1/RATNO_OGs.sam
2025-09-23 15:01:38 DEBUG Running samtools sort -@ 1 -o output/04_mapping_sample_1/RATNO_OGs_sorted.bam output/04_mapping_sample_1/RATNO_OGs.bam
2025-09-23 15:01:38 DEBUG Running samtools sort -@ 1 -o output/04_mapping_sample_1/RATNO_OGs_sorted.bam output/04_mapping_sample_1/RATNO_OGs.bam
2025-09-23 15:01:38 DEBUG samtools index -@ 1 output/04_mapping_sample_1/RATNO_OGs_sorted.bam
2025-09-23 15:01:38 DEBUG Running samtools index -@ 1 output/04_mapping_sample_1/RATNO_OGs_sorted.bam
Mapping reads to species: 60%|████████████████████████████████████████████████▌ | 3/5 [00:01<00:00, 2.17 species/s]2025-09-23 15:01:39 INFO sample_1: --- Mapping of reads to GORGO reference species ---
2025-09-23 15:01:39 DEBUG Running minimap2 -ax sr -t 1 output/02_ref_dna/GORGO_OGs.fa sample_1.fastq sample_2.fastq > output/04_mapping_sample_1/GORGO_OGs.sam
2025-09-23 15:01:39 DEBUG Shell err: b'[M::mm_idx_gen::0.007*1.26] collected minimizers\n[M::mm_idx_gen::0.011*1.17] sorted minimizers\n[M::main::0.011*1.17] loaded/built the index for 20 target sequence(s)\n[M::mm_mapopt_update::0.011*1.17] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 20\n[M::mm_idx_stat::0.012*1.16] distinct minimizers: 6065 (100.00% are singletons); average occurrences: 1.000; average spacing: 6.071; total length: 36819\n[M::worker_pipeline::0.179*1.01] mapped 50000 sequences\n[M::main] Version: 2.30-r1287\n[M::main] CMD: minimap2 -ax sr -t 1 output/02_ref_dna/GORGO_OGs.fa sample_1.fastq sample_2.fastq\n[M::main] Real time: 0.181 sec; CPU: 0.183 sec; Peak RSS: 0.022 GB\n'
2025-09-23 15:01:39 DEBUG mapping with minimap2 -ax sr -t 1 output/02_ref_dna/GORGO_OGs.fa sample_1.fastq sample_2.fastq > output/04_mapping_sample_1/GORGO_OGs.sam
2025-09-23 15:01:39 INFO sample_1: Mapping to GORGO_OGs.fa references took 0.2119908332824707.
2025-09-23 15:01:39 DEBUG samtools view -F 4 -bh -S -@ 1 -o output/04_mapping_sample_1/GORGO_OGs.bam output/04_mapping_sample_1/GORGO_OGs.sam
2025-09-23 15:01:39 DEBUG Running samtools view -F 4 -bh -S -@ 1 -o output/04_mapping_sample_1/GORGO_OGs.bam output/04_mapping_sample_1/GORGO_OGs.sam
2025-09-23 15:01:39 DEBUG Running samtools sort -@ 1 -o output/04_mapping_sample_1/GORGO_OGs_sorted.bam output/04_mapping_sample_1/GORGO_OGs.bam
2025-09-23 15:01:39 DEBUG Running samtools sort -@ 1 -o output/04_mapping_sample_1/GORGO_OGs_sorted.bam output/04_mapping_sample_1/GORGO_OGs.bam
2025-09-23 15:01:39 DEBUG samtools index -@ 1 output/04_mapping_sample_1/GORGO_OGs_sorted.bam
2025-09-23 15:01:39 DEBUG Running samtools index -@ 1 output/04_mapping_sample_1/GORGO_OGs_sorted.bam
Mapping reads to species: 80%|████████████████████████████████████████████████████████████████▊ | 4/5 [00:01<00:00, 2.23 species/s]2025-09-23 15:01:39 INFO sample_1: --- Mapping of reads to XENLA reference species ---
2025-09-23 15:01:39 DEBUG Running minimap2 -ax sr -t 1 output/02_ref_dna/XENLA_OGs.fa sample_1.fastq sample_2.fastq > output/04_mapping_sample_1/XENLA_OGs.sam
2025-09-23 15:01:39 DEBUG Shell err: b'[M::mm_idx_gen::0.005*1.46] collected minimizers\n[M::mm_idx_gen::0.009*1.27] sorted minimizers\n[M::main::0.009*1.27] loaded/built the index for 20 target sequence(s)\n[M::mm_mapopt_update::0.009*1.27] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 20\n[M::mm_idx_stat::0.010*1.25] distinct minimizers: 6123 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.982; total length: 36627\n[M::worker_pipeline::0.177*1.01] mapped 50000 sequences\n[M::main] Version: 2.30-r1287\n[M::main] CMD: minimap2 -ax sr -t 1 output/02_ref_dna/XENLA_OGs.fa sample_1.fastq sample_2.fastq\n[M::main] Real time: 0.181 sec; CPU: 0.183 sec; Peak RSS: 0.022 GB\n'
2025-09-23 15:01:39 DEBUG mapping with minimap2 -ax sr -t 1 output/02_ref_dna/XENLA_OGs.fa sample_1.fastq sample_2.fastq > output/04_mapping_sample_1/XENLA_OGs.sam
2025-09-23 15:01:39 INFO sample_1: Mapping to XENLA_OGs.fa references took 0.21446466445922852.
2025-09-23 15:01:39 DEBUG samtools view -F 4 -bh -S -@ 1 -o output/04_mapping_sample_1/XENLA_OGs.bam output/04_mapping_sample_1/XENLA_OGs.sam
2025-09-23 15:01:39 DEBUG Running samtools view -F 4 -bh -S -@ 1 -o output/04_mapping_sample_1/XENLA_OGs.bam output/04_mapping_sample_1/XENLA_OGs.sam
2025-09-23 15:01:39 DEBUG Running samtools sort -@ 1 -o output/04_mapping_sample_1/XENLA_OGs_sorted.bam output/04_mapping_sample_1/XENLA_OGs.bam
2025-09-23 15:01:39 DEBUG Running samtools sort -@ 1 -o output/04_mapping_sample_1/XENLA_OGs_sorted.bam output/04_mapping_sample_1/XENLA_OGs.bam
2025-09-23 15:01:39 DEBUG samtools index -@ 1 output/04_mapping_sample_1/XENLA_OGs_sorted.bam
2025-09-23 15:01:39 DEBUG Running samtools index -@ 1 output/04_mapping_sample_1/XENLA_OGs_sorted.bam
Mapping reads to species: 100%|█████████████████████████████████████████████████████████████████████████████████| 5/5 [00:02<00:00, 2.22 species/s]
2025-09-23 15:01:39 INFO sample_1: Mapping to all references took 2.2673497200012207.
Adding mapped seq to alignments: 100%|█████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 566797.84 alignments/s]
Adding mapped seq to OG: 100%|████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 693273.39 OGs/s]
--- Add inferred mapped sequence back to OGs ---
Adding mapped seq to OG: 100%|████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 113206.59 OGs/s]
2025-09-23 15:01:39 INFO sample_1: Appending 9 reconstructed sequences to present OG took 0.007883548736572266.
2025-09-23 15:01:40 INFO --- Add inferred mapped sequence back to alignment ---
Adding mapped seq to alignments: 100%|███████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 1185.57 alignments/s]
2025-09-23 15:01:40 INFO sample_1: Appending 3 reconstructed sequences to present Alignments took 0.01756572723388672.
2025-09-23 15:01:40 INFO Running following command: /scratch16/miniconda3/envs/r2tv/bin/iqtree -nt 1 -m LG -mem 4G -pre /tmp/iqtree_ml46wx7e/tmp_output -s /tmp/iqtree_ml46wx7e/tmp_output.phy
2025-09-23 15:01:53 INFO Tree is written to output/tree_sample_1.nwk
2025-09-23 15:01:53 INFO sample_1: Tree inference took 13.006760120391846.
2025-09-23 15:01:53 INFO (sample_1:0.0290631974,((MNELE:0.9368788404,XENLA:0.1448431871):0.1378796564,(HUMAN:0.0039337162,GORGO:0.0103960869):0.0496057322):0.0599756384,RATNO:0.0198668369);
2025-09-23 15:01:53 INFO ------- Read2Tree finished -*- -------
done- main
2025-09-23 15:01:53 INFO sample_1: Time taken 27.540438666939735